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Yang Y, Hu J, Wei X, Huang K, Li C, Yang G. Deciphering core microbiota in rhizosphere soil and roots of healthy and Rhizoctonia solani-infected potato plants from various locations. Front Microbiol 2024; 15:1386417. [PMID: 38585705 PMCID: PMC10995396 DOI: 10.3389/fmicb.2024.1386417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Black scurf caused by Rhizoctonia solani severely affects potato production. Through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA, the study was based on the location (Kunming, Qujing, and Zhaotong), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. We found plant components significantly influence microbial diversity, with rhizosphere soil being more diverse than roots, and the microbial community in the root is mainly derived from the rhizosphere soil. Moreover, the rhizosphere soil and roots of healthy potato plants exhibit greater microbial diversity compared to those of potato plants infected by Rhizoctonia solani. Bacterial phyla Actinobacteriota and Acidobacteriota were enriched in rhizosphere soil compared to that of roots, whereas Proteobacteria and Cyanobacteria showed the opposite trend. Fungal phylum Ascomycota was found in low relative abundance in rhizosphere soil than in roots, whereas Basidiomycota showed the opposite trend. Bacterial genera including Streptomyces, Lysobacter, Bacillus, Pseudomonas, Ensifer, Enterobacter, and the Rhizobium group (Allorhizobium, Neorhizobium, Pararhizobium, Rhizobium), along with fungal genera such as Aspergillus, Penicillium, Purpureocillium, and Gibberella moniliformis, have the potential ability of plant growth promotion and disease resistance. However, most fungal species and some bacterial species are pathogenic to potato and could provide a conducive environment for black scurf infection. Interaction within the bacterial network increased in healthy plants, contrasting with the trend in the fungal network. Our findings indicate that R. solani significantly alters potato plant microbial diversity, underscoring the complexity and potential interactions between bacterial and fungal communities for promoting potato plant health and resistance against black scurf.
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Affiliation(s)
| | | | | | | | | | - Genhua Yang
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
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Liang J, Chen Y, Li S, Liu D, Tian H, Xiang Q, Zhao K, Yu X, Chen Q, Fan H, Zhang L, Penttinen P, Gu Y. Transcriptomic analysis and carbohydrate metabolism-related enzyme expression across different pH values in Rhizopus delemar. Front Microbiol 2024; 15:1359830. [PMID: 38511010 PMCID: PMC10953822 DOI: 10.3389/fmicb.2024.1359830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction pH is one of the important factors affecting the growth and performance of microorganisms. Methods We studied the pH response and plant growth-promoting (PGP) ability of Rhizopus delemar using cultivation experiments and transcriptomics, and verified the expression profiles using quantitative real-time PCR. Results pH affected the growth and PGP properties of R. delemar. At pH 7, the growth rate of R. delemar was rapid, whereas pH 4 and 8 inhibited mycelial growth and PGP ability, respectively. In the pot experiment, the plant height was the highest at pH 7, 56 cm, and the lowest at pH 4 and pH 5, 46.6 cm and 47 cm, respectively. Enzyme activities were highest at pH 6 to pH 7. Enzyme activities were highest at pH 6 to pH 7. Among the 1,629 differentially expressed genes (DEGs), 1,033 genes were up-regulated and 596 were down-regulated. A total of 1,623 DEGs were annotated to carbohydrate-active enzyme coding genes. Discussion The PGP characteristics, e.g., Phosphorus solubilization ability, of R. delemar were strongest at pH 7. The results provide useful information regarding the molecular mechanism of R. delemar pH response.
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Affiliation(s)
- Jinpeng Liang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulan Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Sisi Li
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dongyang Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Hong Tian
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Hongzhu Fan
- Institute of Agricultural Resources and Environmental Science, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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Kim DY, Kim J, Lee YM, Byeon SM, Gwak JH, Lee JS, Shin DH, Park HY. Novel, acidic, and cold-adapted glycoside hydrolase family 8 endo-β-1,4-glucanase from an Antarctic lichen-associated bacterium, Lichenicola cladoniae PAMC 26568. Front Microbiol 2022; 13:935497. [PMID: 35910630 PMCID: PMC9329076 DOI: 10.3389/fmicb.2022.935497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Endo-β-1,4-glucanase is a crucial glycoside hydrolase (GH) involved in the decomposition of cellulosic materials. In this study, to discover a novel cold-adapted β-1,4-D-glucan-degrading enzyme, the gene coding for an extracellular endo-β-1,4-glucanase (GluL) from Lichenicola cladoniae PAMC 26568, an Antarctic lichen (Cladonia borealis)-associated bacterium, was identified and recombinantly expressed in Escherichia coli BL21. The GluL gene (1044-bp) encoded a non-modular polypeptide consisting of a single catalytic GH8 domain, which shared the highest sequence identity of 55% with that of an uncharacterized protein from Gluconacetobacter takamatsuzukensis (WP_182950054). The recombinant endo-β-1,4-glucanase (rGluL: 38.0 kDa) most efficiently degraded sodium carboxymethylcellulose (CMC) at pH 4.0 and 45°C, and showed approximately 23% of its maximum degradation activity even at 3°C. The biocatalytic activity of rGluL was noticeably enhanced by >1.3-fold in the presence of 1 mM Mn2+ or NaCl at concentrations between 0.1 and 0.5 M, whereas the enzyme was considerably downregulated by 1 mM Hg2+ and Fe2+ together with 5 mM N-bromosuccinimide and 0.5% sodium dodecyl sulfate. rGluL is a true endo-β-1,4-glucanase, which could preferentially decompose D-cellooligosaccharides consisting of 3 to 6 D-glucose, CMC, and barley β-glucan, without other additional glycoside hydrolase activities. The specific activity (15.1 U mg–1) and kcat/Km value (6.35 mg–1 s–1mL) of rGluL toward barley β-glucan were approximately 1.8- and 2.2-fold higher, respectively, compared to its specific activity (8.3 U mg–1) and kcat/Km value (2.83 mg–1 s–1mL) toward CMC. The enzymatic hydrolysis of CMC, D-cellotetraose, and D-cellohexaose yielded primarily D-cellobiose, accompanied by D-glucose, D-cellotriose, and D-cellotetraose. However, the cleavage of D-cellopentaose by rGluL resulted in the production of only D-cellobiose and D-cellotriose. The findings of the present study imply that rGluL is a novel, acidic, and cold-adapted GH8 endo-β-1,4-glucanase with high specific activity, which can be exploited as a promising candidate in low-temperature processes including textile and food processes.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- *Correspondence: Do Young Kim,
| | - Jonghoon Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Soo Min Byeon
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biological Science, Daejeon University, Daejeon, South Korea
| | - Jeong Hae Gwak
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jong Suk Lee
- Biocenter, Gyeonggido Business and Science Accelerator (GBSA), Suwon, South Korea
| | | | - Ho-Yong Park
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Ho-Yong Park,
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Mohammadi S, Tarrahimofrad H, Arjmand S, Zamani J, Haghbeen K, Aminzadeh S. Expression, characterization, and activity optimization of a novel cellulase from the thermophilic bacteria Cohnella sp. A01. Sci Rep 2022; 12:10301. [PMID: 35717508 PMCID: PMC9206686 DOI: 10.1038/s41598-022-14651-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
Cellulases are hydrolytic enzymes with wide scientific and industrial applications. We described a novel cellulase, CelC307, from the thermophilic indigenous Cohnella sp. A01. The 3-D structure of the CelC307 was predicted by comparative modeling. Docking of CelC307 with specific inhibitors and molecular dynamic (MD) simulation revealed that these ligands bound in a non-competitive manner. The CelC307 protein was purified and characterized after recombinant expression in Escherichia coli (E. coli) BL21. Using CMC 1% as the substrate, the thermodynamic values were determined as Km 0.46 mM, kcat 104.30 × 10-3 (S-1), and kcat/Km 226.73 (M-1 S-1). The CelC307 was optimally active at 40 °C and pH 7.0. The culture condition was optimized for improved CelC307 expression using Plackett-Burman and Box-Behnken design as follows: temperature 20 °C, pH 7.5, and inoculation concentration with an OD600 = 1. The endoglucanase activity was positively modulated in the presence of Na+, Li+, Ca2+, 2-mercaptoethanol (2-ME), and glycerol. The thermodynamic parameters calculated for CelC307 confirmed its inherent thermostability. The characterized CelC307 may be a suitable candidate for various biotechnological applications.
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Affiliation(s)
- Shima Mohammadi
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Tarrahimofrad
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Javad Zamani
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Kamahldin Haghbeen
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Madubuike H, Ferry N. Characterisation of a Novel Acetyl Xylan Esterase (BaAXE) Screened from the Gut Microbiota of the Common Black Slug ( Arion ater). Molecules 2022; 27:2999. [PMID: 35566348 PMCID: PMC9104356 DOI: 10.3390/molecules27092999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/24/2022] Open
Abstract
Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.
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Affiliation(s)
- Henry Madubuike
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK
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8
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Gavande PV, Nath P, Kumar K, Ahmed N, Fontes CMGA, Goyal A. Highly efficient, processive and multifunctional recombinant endoglucanase RfGH5_4 from Ruminococcus flavefaciens FD-1 v3 for recycling lignocellulosic plant biomasses. Int J Biol Macromol 2022; 209:801-813. [PMID: 35421411 DOI: 10.1016/j.ijbiomac.2022.04.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
Abstract
Gene encoding endoglucanase, RfGH5_4 from R. flavefaciens FD-1 v3 was cloned, expressed in Escherichia coli BL21(DE3) cells and purified. RfGH5_4 showed molecular size 41 kDa and maximum activity at pH 5.5 and 55 °C. It was stable between pH 5.0-8.0, retaining 85% activity and between 5 °C-45 °C, retaining 75% activity, after 60 min. RfGH5_4 displayed maximum activity (U/mg) against barley β-D-glucan (665) followed by carboxymethyl cellulose (450), xyloglucan (343), konjac glucomannan (285), phosphoric acid swollen cellulose (86), beechwood xylan (21.7) and carob galactomannan (16), thereby displaying the multi-functionality. Catalytic efficiency (mL.mg-1 s-1) of RfGH5_4 against carboxymethyl cellulose (146) and konjac glucomannan (529) was significantly high. TLC and MALDI-TOF-MS analyses of RfGH5_4 treated hydrolysates of cellulosic and hemicellulosic polysaccharides displayed oligosaccharides of degree of polymerization (DP) between DP2-DP11. TLC, HPLC and Processivity-Index analyses revealed RfGH5_4 to be a processive endoglucanase as initially, for 30 min it hydrolysed cellulose to cellotetraose followed by persistent release of cellotriose and cellobiose. RfGH5_4 yielded sufficiently high Total Reducing Sugar (TRS, mg/g) from saccharification of alkali pre-treated sorghum (72), finger millet (62), sugarcane bagasse (38) and cotton (27) in a 48 h saccharification reaction. Thus, RfGH5_4 can be considered as a potential endoglucanase for renewable energy applications.
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Affiliation(s)
- Parmeshwar Vitthal Gavande
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Priyanka Nath
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Krishan Kumar
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Nazneen Ahmed
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal; NZYTech - Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício, Lisbon, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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10
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He T, Cheng X, Xing C. The gut microbial diversity of colon cancer patients and the clinical significance. Bioengineered 2021; 12:7046-7060. [PMID: 34551683 PMCID: PMC8806656 DOI: 10.1080/21655979.2021.1972077] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/31/2022] Open
Abstract
The microbial diversity and communities in the excrement of healthy and patients suffered from cancer were identified by 16SrDNA sequencing performed on the Illumina Hi Seq sequencing platform. The microbial difference was also analyzed. The sequencing results showed high quality of the data, and the microbial communities were more various in the excrement of cancer patients. And the abundance of Firmicutes phylum was significantly reduced in cancer group. The phylum of Fermicutes, Bacteroidetes in cancer group are significantly down-regulated and up-regulated compared with normal group. The species of Faecalibacterium prausnitzii, Bateroides vulgatus and Fusicatenibacter saccharivorans are significantly lower in cancer group than that in normal group (P< 0.05). The species of Prevetella copri, M. uniformis, and Escherichia coli are significantly higher in the cancer group than that in normal group. The comparative results indicated that beneficial bacterium significantly decreased in colorectal cancer (CRC) group, and harmful bacterium significantly increased in the colon cancer group, meanwhile the acidity, sugar increased whereas the oxygen content decreased to facilitate the growth of harmful bacterium. The results would provide microbial approaches for the treatment of colon cancer by the intake of beneficial microbial communities.
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Affiliation(s)
- Tengfei He
- Department of Genenal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaohui Cheng
- Department of Genenal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chungen Xing
- Department of Genenal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
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11
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Verdel N, Rijavec T, Rybkin I, Erzin A, Velišček Ž, Pintar A, Lapanje A. Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills. Front Microbiol 2021; 12:758702. [PMID: 34671337 PMCID: PMC8521037 DOI: 10.3389/fmicb.2021.758702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
In the wood-free paper industry, whitewater is usually a mixture of additives for paper production. We are currently lacking an efficient, cost-effective purification technology for their removal. In closed whitewater cycles the additives accumulate, causing adverse production problems, such as the formation of slime and pitch. The aim of our study was to find an effective bio-based strategy for whitewater treatment using a selection of indigenous bacterial isolates. We first obtained a large collection of bacterial isolates and then tested them individually by simple plate and spectrophotometric methods for their ability to degrade the papermaking additives, i.e., carbohydrates, resin acids, alkyl ketene dimers, polyvinyl alcohol, latex, and azo and fluorescent dyes. We examined correlation between carbon source use, genera, and inoculum source of isolates using two multivariate methods: principal component analysis and FreeViz projection. Of the 318 bacterial isolates, we selected a consortium of four strains (Xanthomonadales bacterium sp. CST37-CF, Sphingomonas sp. BLA14-CF, Cellulosimicrobium sp. AKD4-BF and Aeromonas sp. RES19-BTP) that degrade the entire spectrum of tested additives by means of dissolved organic carbon measurements. A proof-of-concept study on a pilot scale was then performed by immobilizing the artificial consortium of the four strains and inserting them into a 33-liter, tubular flow-through reactor with a retention time of < 15 h. The consortium caused an 88% reduction in the COD of the whitewater, even after 21 days.
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Affiliation(s)
- Nada Verdel
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Iaroslav Rybkin
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Anja Erzin
- Faculty of Chemistry and Chemical Technology, Graduate School, University of Ljubljana, Ljubljana, Slovenia
| | | | - Albin Pintar
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
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Wang Y, Wang C, Chen Y, Chen B, Guo P, Cui Z. Metagenomic Insight into Lignocellulose Degradation of the Thermophilic Microbial Consortium TMC7. J Microbiol Biotechnol 2021; 31:1123-1133. [PMID: 34226407 PMCID: PMC9706030 DOI: 10.4014/jmb.2106.06015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022]
Abstract
Biodegradation is the key process involved in natural lignocellulose biotransformation and utilization. Microbial consortia represent promising candidates for applications in lignocellulose conversion strategies for biofuel production; however, cooperation among the enzymes and the labor division of microbes in the microbial consortia remains unclear. In this study, metagenomic analysis was performed to reveal the community structure and extremozyme systems of a lignocellulolytic microbial consortium, TMC7. The taxonomic affiliation of TMC7 metagenome included members of the genera Ruminiclostridium (42.85%), Thermoanaerobacterium (18.41%), Geobacillus (10.44%), unclassified_f__Bacillaceae (7.48%), Aeribacillus (2.65%), Symbiobacterium (2.47%), Desulfotomaculum (2.33%), Caldibacillus (1.56%), Clostridium (1.26%), and others (10.55%). The carbohydrate-active enzyme annotation revealed that TMC7 encoded a broad array of enzymes responsible for cellulose and hemicellulose degradation. Ten glycoside hydrolases (GHs) endoglucanase, 4 GHs exoglucanase, and 6 GHs β-glucosidase were identified for cellulose degradation; 6 GHs endo-β-1,4-xylanase, 9 GHs β-xylosidase, and 3 GHs β-mannanase were identified for degradation of the hemicellulose main chain; 6 GHs arabinofuranosidase, 2 GHs α-mannosidase, 11 GHs galactosidase, 3 GHs α-rhamnosidase, and 4 GHs α-fucosidase were identified as xylan debranching enzymes. Furthermore, by introducing a factor named as the contribution coefficient, we found that Ruminiclostridium and Thermoanaerobacterium may be the dominant contributors, whereas Symbiobacterium and Desulfotomaculum may serve as "sugar cheaters" in lignocellulose degradation by TMC7. Our findings provide mechanistic profiles of an array of enzymes that degrade complex lignocellulosic biomass in the microbial consortium TMC7 and provide a promising approach for studying the potential contribution of microbes in microbial consortia.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China
| | - Chen Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Yonglun Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Beibei Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R. China
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13
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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14
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Joshi N, Kaushal G, Singh SP. Biochemical characterization of a novel thermo-halo-tolerant GH5 endoglucanase from a thermal spring metagenome. Biotechnol Bioeng 2021; 118:1531-1544. [PMID: 33410140 DOI: 10.1002/bit.27668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/31/2022]
Abstract
A novel endoglucanase gene, celM , was cloned from a thermal spring metagenome. The gene was expressed in Escherichia coli, and the protein was extracted and purified. The protein catalyzed the hydrolysis of amorphous cellulose in a wide range of temperatures, 30-95°C, with optimal activity at 80°C. It was able to tolerate high temperature (80°C) with a half-life of 8 h. Its activity was eminent in a wide pH range of 3.0-11.0, with the highest activity at pH 6.0. The enzyme was tested for halostability. Any significant loss was not recorded in the activity of CelM after the exposure to salinity (3 M NaCl) for 30 days. Furthermore, CelM displayed a substantial resistance toward metal ions, denaturant, reducing agent, organic solvent, and non-ionic surfactants. The amorphous cellulose, treated with CelM , was randomly cleaved, generating cello-oligosaccharides of 2-5 degree of polymerization. Furthermore, CelM was demonstrated to catalyze the hydrolysis of cellulose fraction in the delignified biomass samples, for example, sweet sorghum bagasse, rice straw, and corncob, into cello-oligosaccharides. Given that CelM is a thermo-halo-tolerant GH5 endoglucanase, with resistance to detergents and organic solvent, the biocatalyst could be of potential usefulness for a variety of industrial applications.
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Affiliation(s)
- Namrata Joshi
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
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15
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A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions. BMC Biotechnol 2020; 20:56. [PMID: 33076889 PMCID: PMC7574624 DOI: 10.1186/s12896-020-00647-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Background Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant. Results The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including Vmax, Km, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg2+, Mn2+, Cu2+, Fe2+ and Ca2+. Our results showed that treatment with MnCl2 could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5). Conclusion Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.
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16
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Zhan M, Wang L, Xie C, Fu X, Zhang S, Wang A, Zhou Y, Xu C, Zhang H. Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism. Front Microbiol 2020; 11:551038. [PMID: 33072012 PMCID: PMC7537565 DOI: 10.3389/fmicb.2020.551038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Chunyu Xie
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
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17
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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